feat: add types (#55)

* feat: add types

* fix: unnamed functions

Author: jobo322

ml-gsd.d.ts

@@ -0,0 +1,147 @@
+export interface XYNumberArray {
+  x: Array<number> | Float64Array;
+  y: Array<number> | Float64Array;
+}
+
+interface GsdOptions {
+  /**
+   * Noise threshold in spectrum y units. Default is three/thresholdFactor times the absolute median of data.y.
+   * @default `median(data.y) * (options.thresholdFactor || 3)`
+   */
+  noiseLevel?: number;
+  /**
+   * Threshold to determine if a given peak should be considered as a noise, bases on its relative height compared to the highest peak.
+   * @default 0.01
+   */
+  minMaxRatio?: number;
+  /**
+   * If broadRatio is higher than 0, then all the peaks which second derivative smaller than broadRatio * maxAbsSecondDerivative will be marked with the soft mask equal to true.
+   * @default 0.00025
+   */
+  broadRatio?: number;
+  /**
+   * Select the peak intensities from a smoothed version of the independent variables.
+   * @default true
+   */
+  smoothY?: boolean;
+  /**
+   * if it is true, it optimizes the x and intensity by extrapolation.
+   * @default false
+   */
+  realTopDetection?: boolean;
+  /**
+   * options to shape used to adapt the FWHM
+   * @default {kind:'gaussian'}
+   */
+  shape?: { kind: string };
+  // /**
+  //  * Threshold to determine if some peak is candidate to clustering into range.
+  //  * @default 0.25
+  //  */
+  // broadWidth: number;
+  /**
+   * Options for savitz Golay
+   */
+  sgOptions?: { windowSize: number; polynomial: number };
+  /**
+   * filter based on intensity of the first derive.
+   * @default -1;
+   */
+}
+
+export interface Peak {
+  x: number;
+  y: number;
+  width: number;
+  left?: number;
+  right?: number;
+  base?: number;
+  soft?: boolean;
+  kind?: string;
+}
+
+export interface OptimizePeaksOptions {
+  /**
+   * factor to determine the width at the moment to group the peaks in signals in 'GSD.optimizePeaks' function.
+   * @default 1
+   */
+  factorWidth?: number;
+  /**
+   * times of width to use to optimize peaks
+   * @default 2
+   */
+  factorLimits?: number;
+  /**
+   * options to shape used to adapt the FWHM
+   * @default {kind:'gaussian'}
+   */
+  shape?: { kind: string };
+  /**
+   * options for optimization step
+   */
+  optimization?: OptimizationOptions;
+}
+
+export interface OptimizationOptions {
+  /**
+   * represent the algorithm to optimize.
+   * @default {kind:'lm'}
+   */
+  kind?: string;
+  /**
+   * Time limit to stop the optimization in seconds.
+   * @default 10
+   */
+  timeout?: number
+}
+
+export interface OptimizedPeak {
+  x: number;
+  y: number;
+  width: number;
+  mu?: number;
+}
+
+export function gsd(data: XYNumberArray, options?: GsdOptions): Peak[];
+
+export function optimizePeaks(
+  data: XYNumberArray,
+  peakList: Peak[],
+  options?: OptimizePeaksOptions,
+): OptimizedPeak[];
+
+export function joinBroadPeaks(
+  peakList: Peak[],
+  options?: JoinBroadPeaksOptions,
+): Peak[];
+
+export interface JoinBroadPeaksOptions {
+  /**
+   * @default 0.25
+   */
+  width: number;
+  /**
+   * @default { kind: 'gaussian' }
+   */
+  shape: { kind: string };
+  /**
+   * @default { kind: 'lm', timeout: 10 }
+   */
+  optimization: OptimizationOptions;
+}
+
+export function groupPeaks(peakList: Peak[], factor?: number): Peak[][];
+
+export function broadenPeaks(
+  peakList: Peak[],
+  options?: {
+    /**
+     * @default 2
+     */
+    factor: number;
+    /**
+     * @default false
+     */
+    overlap: boolean;
+  },
+): Peak[];

package.json

@@ -4,6 +4,7 @@
   "description": "Global Spectra Deconvolution",
   "main": "lib/index.js",
   "module": "src/index.js",
+  "types": "ml-gsd.d.ts",
   "files": [
     "lib",
     "src"

src/__tests__/infraRed.js

@@ -2,9 +2,9 @@ import { readFileSync } from 'fs';
 
 import { gsd } from '..';
 
-describe('Global spectra deconvolution Infrared spectra', function () {
+describe('Global spectra deconvolution Infrared spectra', () => {
   // Test case obtained from Pag 443, Chap 8.
-  it('Should get the correct result', function () {
+  it('Should get the correct result', () => {
     let spectrum = JSON.parse(
       readFileSync(`${__dirname}/data/infraRed.json`, 'utf-8'),
     );

src/gsd.js

@@ -131,7 +131,6 @@ export function gsd(data, options = {}) {
   // By the intermediate value theorem We cannot find 2 consecutive maximum or minimum
   for (let i = 1; i < yData.length - 1; ++i) {
     // filter based on derivativeThreshold
-    // console.log('pasa', y[i], dY[i], ddY[i]);
     if (Math.abs(dY[i]) > derivativeThreshold) {
       // Minimum in first derivative
       if (
@@ -237,7 +236,7 @@ export function gsd(data, options = {}) {
     signals[j].base = noiseLevel;
   }
 
-  signals.sort(function (a, b) {
+  signals.sort((a, b) => {
     return a.x - b.x;
   });
 

src/post/joinBroadPeaks.js

@@ -79,7 +79,7 @@ export function joinBroadPeaks(peakList, options = {}) {
       count = 1;
     }
   }
-  peakList.sort(function (a, b) {
+  peakList.sort((a, b) => {
     return a.x - b.x;
   });